ConcatStringTogether

Script

import java.io.BufferedOutputStream;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
import java.io.FileWriter;
import java.util.List;
import java.util.Scanner;
 
	// create a new string for storing the sequence 
 	out1 = new String();
	// create a file output stream from the provided output file location 
			FileOutputStream out = null;
            out = new FileOutputStream(new File(SeqFileURL));
			getSequence =new Scanner(new File(FastaFileURL));
	// temporary virable
			byte[] s3={};
  			String s = getSequence.next();
	// concat all the information into a whole string	
		while (getSequence.hasNext())
			{
				if (s.charAt(0)=='>')
				{
					s=getSequence.next();
				}	
				else{
				out1 = out1.concat(s);				
s3 = s.getBytes();

				out.write(s3);
				s=getSequence.next();
				}
			}

			if (s.charAt(0)!='>')
			{
				out1 = out1.concat(s);	
			s3 = s.getBytes();
			out.write(s3);
			}
			
			out.close();